def parse_cmdline_args(cmdlineargs=None):
'''Parses command line arguments.
Args:
cmdlineargs: List of command line arguments. When None, arguments in
sys.argv are parsed (Default: None).
'''
parser = optparse.OptionParser(usage=USAGE)
msg = 'file containing lattice vectors (overrides lattice vectors'\
' in the geometry file)'
parser.add_option(
'-l', '--lattice-file', action='store', help=msg, dest='latticefile')
msg = 'output file to store the resulting geometry'
parser.add_option('-o', '--output', action='store', default='-', help=msg)
options, args = parser.parse_args(cmdlineargs)
if len(args) != 4:
raise ScriptError('Incorrect number of arguments')
infile = args[0]
reps = []
for repstr in args[1:4]:
try:
reps.append(int(repstr))
except ValueError:
msg = "Invalid repetition number '" + repstr + "'."
raise ScriptError(msg)
if not (reps[0] > 0 and reps[1] > 0 and reps[2] > 0):
raise ScriptError('Repetition numbers must be greater than zero')
return infile, (reps[0], reps[1], reps[2]), options
def repeatgen(infile, repeats, options):
'''Repeats geometry from gen files.
Args:
infile: File containing the gen-formatted geometry.
repeats: (n1, n2, n3) integer tuple containing the repetitions along
each lattice vector.
options: Options (e.g. as returned by the command line parser).
'''
gen = Gen.fromfile(infile)
geo = gen.geometry
latvecs = geo.latvecs
if options.latticefile:
latvecs = np.fromfile(options.latticefile, sep=' ')
if len(latvecs) != 9:
msg = ('Invalid number of lattice vector components in '
+ options.latticefile)
raise ScriptError(msg)
latvecs.shape = (3, 3)
if latvecs is None:
msg = 'No lattice vectors found (neither in gen nor in external file)'
raise ScriptError(msg)
newgeo = _repeatgeo(geo, latvecs, repeats)
newgen = Gen(newgeo, gen.fractional)
outfile = options.output
if outfile == '-':
outfile = sys.stdout
newgen.tofile(outfile)
def parse_cmdline_args(cmdlineargs=None):
'''Parses command line arguments.
Args:
cmdlineargs: List of command line arguments. When None, arguments in
sys.argv are parsed. (Default: None)
'''
parser = optparse.OptionParser(usage=USAGE)
parser.add_option("-o", "--output", action="store", dest="output",
default='-', help="override the name of the output file "
"(use '-' for standard out")
parser.add_option("-c", "--component", action="store", dest="component",
type=str, default='I', help="strain type to apply "
"posible values being xx, yy, zz, xz, xz, yz or I for "
"isotropic (default value: I)")
options, args = parser.parse_args(cmdlineargs)
if options.component.lower() not in LABELS:
msg = "Invalid strain component '" + options.component + "'"
raise ScriptError(msg)
if len(args) != 2:
raise ScriptError("You must specify exactly two arguments "
"(input file, strain).")
infile = args[0]
try:
strain = float(args[1])
except ValueError:
raise ScriptError("Invalid strain value '" + args[1] + "'")
if options.component.lower() in ('xx', 'yy', 'zz', 'i') and strain <= -100:
raise ScriptError("Compressive strain cannot exceed 100%")
return infile, strain, options
def parse_cmdline_args(cmdlineargs=None):
'''Parses command line arguments.
Args:
cmdlineargs: List of command line arguments. When None, arguments in
sys.argv are parsed. (Default: None)
'''
parser = argparse.ArgumentParser(description=USAGE)
msg = "override the name of the output file (use '-' for standard out)"
parser.add_argument("-o", "--output", action="store", dest="output",
default='-', help=msg)
msg = "strain type to apply posible values being xx, yy, zz, xz, xz, yz or"\
" I for isotropic (default value: I)"
parser.add_argument("-c", "--component", action="store", dest="component",
type=str, default='I', help=msg)
msg = "input file name"
parser.add_argument("infile", metavar="INPUT", help=msg)
msg = "strain to apply as positive or negative percentage"
parser.add_argument("strain", type=float, metavar="STRAIN", help=msg)
args = parser.parse_args(cmdlineargs)
if args.component.lower() not in LABELS:
msg = "Invalid strain component '" + args.component + "'"
raise ScriptError(msg)
strain = args.strain
if args.component.lower() in ('xx', 'yy', 'zz', 'i') and strain <= -100:
raise ScriptError("Compressive strain cannot exceed 100%")
return args, strain
def gen2cif(args):
'''Converts the given INPUT file in DFTB+ GEN format to CIF format.
Args:
args: Namespace of command line arguments
'''
infile = args.infile
try:
gen = Gen.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
geometry = gen.geometry
if not geometry.periodic:
geometry.setlattice(args.cellsize * np.eye(3))
cif = Cif(gen.geometry)
if args.output:
if args.output == "-":
outfile = sys.stdout
else:
outfile = args.output
else:
if infile.endswith(".gen"):
outfile = infile[:-4] + ".cif"
else:
outfile = infile + ".cif"
cif.tofile(outfile)
def xyz2gen(args):
'''Converts the given INPUT file in XYZ format to DFTB+ GEN format.
Args:
args: Namespace of command line arguments
'''
infile = args.infile
try:
xyz = Xyz.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
geo = xyz.geometry
if args.lattfile:
fp = open(args.lattfile, "r")
tmp = np.fromfile(fp, count=9, dtype=float, sep=" ")
latvecs = tmp.reshape((3, 3))
fp.close()
geo.setlattice(latvecs)
gen = Gen(geo, fractional=args.fractional)
if args.output:
if args.output == "-":
outfile = sys.stdout
else:
outfile = args.output
else:
if infile.endswith(".xyz"):
outfile = infile[:-4] + ".gen"
else:
outfile = infile + ".gen"
gen.tofile(outfile)
def gen2xyz(args):
'''Converts the given INPUT file in DFTB+ GEN format to XYZ format.
Args:
args: Namespace of command line arguments
'''
infile = args.infile
try:
gen = Gen.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
xyz = Xyz(gen.geometry, args.comment)
if args.output:
if args.output == "-":
outfile = sys.stdout
else:
outfile = args.output
else:
if infile.endswith(".gen"):
outfile = infile[:-4] + ".xyz"
else:
outfile = infile + ".xyz"
xyz.tofile(outfile)
if gen.geometry.periodic and args.lattfile:
fp = open(args.lattfile, "w")
for vec in gen.geometry.latvecs:
fp.write("{0:18.10E} {1:18.10E} {2:18.10E}\n".format(*vec))
fp.close()
def parse_cmdline_args(cmdlineargs=None):
'''Parses command line arguments.
Args:
cmdlineargs: List of command line arguments. When None, arguments in
sys.argv are parsed (Default: None).
'''
parser = argparse.ArgumentParser(description=USAGE)
msg = 'file containing lattice vectors (overrides lattice vectors'\
' in the geometry file)'
parser.add_argument('-l',
'--lattice-file',
action='store',
help=msg,
dest='latticefile')
msg = 'output file to store the resulting geometry'
parser.add_argument('-o',
'--output',
action='store',
default='-',
help=msg)
msg = 'create a repeat geometry for phonon bandstructure'
parser.add_argument('-p',
'--phonons',
action='store_true',
default=False,
help=msg)
msg = 'input file name'
parser.add_argument("infile", metavar="INPUT", help=msg)
msg = 'repetition along the first lattice vector'
parser.add_argument('n1', type=int, metavar="N1", help=msg)
msg = 'repetition along the second lattice vector'
parser.add_argument('n2', type=int, metavar="N2", help=msg)
msg = 'repetition along the third lattice vector'
parser.add_argument('n3', type=int, metavar="N3", help=msg)
args = parser.parse_args(cmdlineargs)
if not (args.n1 > 0 and args.n2 > 0 and args.n3 > 0):
raise ScriptError('Repetition numbers must be greater than zero')
if args.phonons:
if (args.n1 % 2 == 0 or args.n2 % 2 == 0 or args.n3 % 2 == 0):
raise ScriptError('Repetition numbers must be odd numbers')
return args
def dp_bands(args):
'''Converts band structure information of DFTB+ output to NXY-format.
Args:
args: Namespace of command line arguments
'''
infile = args.infile
outprefix = args.outprefix
try:
bandout = BandOut.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
if args.spinsep:
# Create filename for each spin-channel
fnames = [
"{0}_s{1:d}.dat".format(outprefix, ispin)
for ispin in range(1, bandout.nspin + 1)
]
plotvals = bandout.eigvalarray[:, :, :, 0]
else:
# Put all eigenvalues in one channel, if no spin separation required
eigvals = bandout.eigvalarray[:, :, :, 0]
plotvals = np.empty(
(1, eigvals.shape[1], eigvals.shape[2] * eigvals.shape[0]),
dtype=float)
for ispin in range(bandout.nspin):
istart = ispin * bandout.nstate
iend = (ispin + 1) * bandout.nstate
plotvals[0, :, istart:iend] = eigvals[ispin, :, :]
fnames = [
outprefix + "_tot.dat",
]
if args.enum:
formstr0 = "{0:d} "
tmp = [
"{" + str(ii) + ":18.10E}"
for ii in range(1, plotvals.shape[2] + 1)
]
formstr = formstr0 + " ".join(tmp) + "\n"
else:
tmp = ["{" + str(ii) + ":18.10E}" for ii in range(plotvals.shape[2])]
formstr = " ".join(tmp) + "\n"
for iout, data in enumerate(plotvals):
fp = open(fnames[iout], "w")
for ik, kdata in enumerate(data):
if args.enum:
fp.write(formstr.format(ik + 1, *kdata))
else:
fp.write(formstr.format(*kdata))
fp.close()
def repeatgen(args):
'''Repeats geometry from gen files.
Args:
args: Namespace of command line arguments
'''
infile = args.infile
repeats = [args.n1, args.n2, args.n3]
try:
gen = Gen.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
geo = gen.geometry
latvecs = geo.latvecs
if args.latticefile:
latvecs = np.fromfile(args.latticefile, sep=' ')
if len(latvecs) != 9:
msg = ('Invalid number of lattice vector components in ' +
args.latticefile)
raise ScriptError(msg)
latvecs.shape = (3, 3)
if latvecs is None:
msg = 'No lattice vectors found (neither in gen nor in external file)'
raise ScriptError(msg)
if args.phonons:
newgeo = _repeatgeo2(geo, latvecs, repeats)
else:
newgeo = _repeatgeo(geo, latvecs, repeats)
newgen = Gen(newgeo, gen.fractional)
outfile = args.output
if outfile == '-':
outfile = sys.stdout
newgen.tofile(outfile)
def straingen(args, strain):
'''Strains a geometry from a gen file.
Args:
args: Namespace of command line arguments
strain: Strain to apply
'''
infile = args.infile
try:
gen = Gen.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
geometry = gen.geometry
strainmtx = np.zeros((3, 3), dtype=float)
for jj in range(3):
strainmtx[jj][jj] = 1.0
components = LABELS[args.component.lower()]
for ii in components:
strainmtx[VOIGHT[ii][0]][VOIGHT[ii][1]] += 0.005 * strain
strainmtx[VOIGHT[ii][1]][VOIGHT[ii][0]] += 0.005 * strain
if geometry.latvecs is not None:
geometry.latvecs = np.dot(geometry.latvecs, strainmtx)
geometry.coords = np.dot(geometry.coords, strainmtx)
if args.output:
if args.output == "-":
outfile = sys.stdout
else:
outfile = args.output
else:
if infile.endswith(".gen"):
outfile = infile
else:
outfile = infile + ".gen"
gen = Gen(geometry, fractional=gen.fractional)
gen.tofile(outfile)
def parse_arguments(cmdlineargs=None):
'''Parses command line arguments.
Args:
cmdlineargs: List of command line arguments. When None, arguments in
sys.argv are parsed (Default: None).
'''
parser = argparse.ArgumentParser(description=USAGE)
msg = "grid separation (default: {0:.2f})".format(DEFAULT_GRID_SEPARATION)
parser.add_argument("-g",
"--gridres",
type=float,
dest="gridres",
default=DEFAULT_GRID_SEPARATION,
help=msg)
msg = "create pdos or occupation weighted dos"
parser.add_argument("-w",
"--weight-occ",
action="store_true",
dest="occweight",
default=False,
help=msg)
msg = "broadening function (default: gauss)"
parser.add_argument("-f",
"--broadening-function",
dest="broadening",
choices=BROADENING_FUNCTIONS,
default=GAUSS_BROADENING,
help=msg)
msg = "order of mp function"
parser.add_argument("-o", "--mporder", type=int, dest="mporder", help=msg)
msg = "broadening width sigma (default: gauss {:.2f}, fermi {:.2f}, "\
"mp {:.2f})".format(DEFAULT_WIDTHS[GAUSS_BROADENING],
DEFAULT_WIDTHS[FERMI_BROADENING],
DEFAULT_WIDTHS[MP_BROADENING])
parser.add_argument("-b",
"--broadening-width",
type=float,
metavar="WIDTH",
dest="broadwidth",
help=msg,
default=-1.0)
msg = "number of sigmas after which the broadening function is considered "\
"to be zero (default: gauss {0:.2f}, fermi {1:.2f}, mp {1:.2f})"\
.format(DEFAULT_RANGES[GAUSS_BROADENING],
DEFAULT_RANGES[FERMI_BROADENING],
DEFAULT_RANGES[MP_BROADENING])
parser.add_argument("-s",
"--sigma-range",
type=float,
metavar="RANGE",
dest="broadrange",
default=-1.0,
help=msg)
msg = "turn on verbose operation"
parser.add_argument("-v",
"--verbose",
action="store_true",
dest="verbose",
default=False,
help=msg)
msg = "input file name"
parser.add_argument("infile", metavar="INPUT", help=msg)
msg = "output file name"
parser.add_argument("outfile", metavar="OUTPUT", help=msg)
args = parser.parse_args(cmdlineargs)
if args.mporder:
if args.broadening != 'mp':
msg = '--mporder can only be set when --broadening-function=mp.'
raise ScriptError(msg)
if args.mporder < 1:
raise ScriptError(msg)
infile = args.infile
outfile = args.outfile
broadening = args.broadening
if args.broadwidth < 0.0:
sigma = DEFAULT_WIDTHS[broadening]
else:
sigma = args.broadwidth
if args.broadrange < 0.0:
sigmarange = DEFAULT_RANGES[broadening]
else:
sigmarange = args.broadrange
return args, broadening, sigma, sigmarange, infile, outfile
def dp_dos(args, broadening, sigma, sigmarange, infile, outfile):
'''convolves the eigenlevels with a broadening function to produce nice
DOS/PDOS curves.
Args:
args: Containing the obtained parsed arguments.
broadening: Specified broadening width sigma.
sigma: Broadening width
sigmarange: number of sigmas after which the broadening function is
considered to be zero
infile: File containing the DFTB+ band structure information.
outfile: Output file name
'''
try:
bandout = BandOut.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
eigvals = bandout.eigvalarray
if not args.occweight:
eigvals[:, :, :, 1] = 1.0
if broadening == FERMI_BROADENING:
aa = 0.5 / sigma
bb = 1.0 / sigma
broadening_function = lambda x: 1.0 / (1.0 + np.cosh(bb * x))
elif broadening == GAUSS_BROADENING:
aa = 1.0 / (sigma * np.sqrt(np.pi))
bb = -1.0 / sigma**2
broadening_function = lambda x: np.exp(bb * x * x)
else: # Methfessel-Paxton
aa = 1.0 / sigma
bb = 1.0 / sigma
order = args.mporder + 1 # order = 0 => Gaussian
coefs = np.zeros(2 * order, dtype=float)
for ii in range(order):
coefs[2*ii] = ((-1)**ii) / (math.factorial(ii) * (4**ii) \
* math.sqrt(math.pi))
broadening_function = lambda x: H.hermval(bb * x, coefs) \
* np.exp(-x * x * bb * bb)
dsigma = sigmarange * sigma
gridres = args.gridres
minval = np.min(eigvals[:, :, :, 0]) - dsigma
maxval = np.max(eigvals[:, :, :, 0]) + dsigma
if args.verbose:
if broadening == GAUSS_BROADENING:
print("Gaussian broadening")
elif broadening == FERMI_BROADENING:
print("Fermi-function compatible broadening")
else:
print("Methfessel-Paxton compatible broadening")
print("Broadening by {0:.2f} eV".format(sigma))
if args.occweight:
print("Weighting DOS by second column of data")
print("Plotting from {0:.2f} eV to {1:.2f} eV".format(minval, maxval))
print("Sigma window is : {0:.2f} eV with a grid resolution of {1:.2f}".
format(dsigma, gridres))
# First and last grid points, x-grid
xmin = np.floor((minval) / gridres) * gridres
xmax = np.ceil((maxval) / gridres) * gridres
xvals = np.arange(xmin, xmax + gridres, gridres, dtype=float)
nval = len(xvals)
# Empty container for y-values
yvals = np.zeros((bandout.nspin, nval), dtype=float)
# Calculate broadened values around each state on the grid.
for ispin in range(bandout.nspin):
for ik in range(bandout.nkpt):
prefac = aa * bandout.kweights[ispin, ik]
for eigval, occ in eigvals[ispin, ik]:
# Grid points for the current curve (first, last)
ilower = int(np.floor((eigval - dsigma - xmin) / gridres))
iupper = int(np.ceil((eigval + dsigma - xmin) / gridres))
dx = eigval - xvals[ilower:iupper + 1]
yvals[ispin, ilower:iupper + 1] += ((prefac * occ) *
broadening_function(dx))
# Write resulting DOS
fp = open(outfile, "w")
if bandout.nspin == 1:
for xx, yy in zip(xvals, yvals[0]):
fp.write("{0:18.10E} {1:18.10E}\n".format(xx, yy))
else:
ytotal = np.sum(yvals, axis=0)
formstr0 = "{0:18.10E} "
tmp = [
"{" + "{0:d}".format(ii) + ":18.10E}"
for ii in range(1, bandout.nspin + 2)
]
formstr = formstr0 + " ".join(tmp) + "\n"
nvals = len(xvals)
for ii in range(nvals):
fp.write(formstr.format(xvals[ii], ytotal[ii], *yvals[:, ii]))
fp.close()
